MDM RNA-seq Analysis Report

Author

Antoine Chaillon

Published

1 December 2025

Note

RNAseq data from Adam Fields’ Laboratory, University of California San Diego (UCSD).

Summary

  • Number of samples: 180
  • Groups: HIV- moderate cannabis, HIV- daily cannabis, HIV- naive to cannabis, HIV+ naive to cannabis, HIV+ daily cannabis, HIV+ moderate cannabis
  • Treatments: CBD, CBDpIL1B, IL1B, THC, THCpIL1B, Vehicle
  • HIV status: HIVn, HIVp
  • Cannabis use: moderate, daily, naive

Workflow Overview

We processed the RNA-seq data from monocyte-derived macrophages (MDMs) using the following pipeline:

DESeq2 Model

The differential expression model used:

design(dds) ~ treatment + hiv_status + cannabis
  • treatment: vehicle, IL1b, CBD, THC, CBD+IL1B, THC+IL1b
  • hiv_status: HIV- vs HIV+
  • cannabis: naive, moderate, daily

Results

Volcano Plots

volcano_list[["cannabis_daily_vs_naive"]]

PCA Plots

using ntop=500 top features by variance

using ntop=500 top features by variance

using ntop=500 top features by variance

using ntop=500 top features by variance

Top Genes Tables

DT::datatable(top20_list[["cannabis_daily_vs_naive"]], options = list(pageLength = 5, scrollX = TRUE), rownames = FALSE)
Note
  • Only genes with padj < 0.05 and |log2FC| > 1 are labeled in volcano plots.
  • PCA plots can be faceted by hiv_status to observe group separation.
  • Interactive tables allow scrolling and sorting top genes for each contrast.
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